The present study aimed to: (i) identify helminth eggs and protozoan cysts in wastewater samples to which both human and animals could be exposed when they are reused in agriculture; and (ii) evaluate the efficiency of their removal by two wastewater treatment systems (activated sludge and lagoon). For these purposes, 234 wastewater samples (117 raw, 117 treated) were collected from 20 wastewater treatment plants (WWTPs) in Tunisia over a one-year sampling period. Parasitic load was enumerated by the modified Bailenger method. The results showed that helminth eggs found were Nematodes mainly represented by Ascaris sp. (95%), Hookworm species (50%), and Enterobius vermicularis (45%). For Cestodes, species identified were Taeniid eggs (85%), Hymenolepis nana (70%), Hymenolepis diminuta (55%) and digestive Strongyles. Among protozoa, Giardia sp., Entamoeba histolytica/dispar/moshkovskii and Entamoeba coli cysts were found in 100% of raw wastewater samples. The overall removal efficiency of helminth eggs and protozoan cysts in the treatment plants ranged from 56.5 to 100% and from 50.4 to 95.5%, respectively. The result from Multiple Correspondence Analysis (MCA) shows that the close clustering of the parasitic mean removal levels indicates that there is little difference in wastewater treatment processes between the WWTPs examined.